Repeat masker - how to use it for estimating repeat expression levels?

[Alex234]

Hello,

I have read about people using repeat masker files to actually look at expression of repeat elements (e.g. in RNA-Seq analysis), but could anyone briefly tell me how to do this? Or with Repbase files?

All I can find on repeat masker on this forum, is how to use it to mask out repeats (which I thought alignment programs did anyway!).


Greatly appreciate any help

Alex